Recombination in the threespine stickleback genome - patterns and consequences

Heterogeneity in recombination rate may strongly influence genome evolution andentail methodological challenges to genomic investigation. Nevertheless, a solid understandingof these issues awaits detailed information across a broad range of taxa.Based on 282 F2 individuals and 1872 single nucleotide polymorphisms, we characterizerecombination in the threespine stickleback fish genome. We find an averagegenome-wide recombination rate of 3.11 cM/Mb. Crossover frequencies are dramaticallyelevated in the chromosome peripheries as compared to the centres, and are consistentwith one obligate crossover per chromosome (but not chromosome arm). Along the sexchromosome, we show that recombination is restricted to a small pseudoautosomaldomain of c. 2 Mb, spanning only 10% of that chromosome. Comparing female to maleRAD sequence coverage allows us to identify two discrete levels of degeneration onthe Y chromosome, one of these ‘evolutionary strata’ coinciding with a previouslyinferred inverted region. Using polymorphism data from two young (>10 000 yearsold) ecologically diverged lake-stream population pairs, we demonstrate that recombinationrate correlates with both the magnitude of allele frequency shifts between populationsand levels of genetic diversity within populations. These associations reflectgenome-wide heterogeneity in the influence of selection on linked sites. We furtherfind a strong relationship between recombination rate and GC content, possibly drivenby GC-biased gene conversion. Overall, we highlight that heterogeneity in recombinationrate has profound consequences on genome evolution and deserves wider recognitionin marker-based genomic analyses.